奶牛瘤胃微生物蛋白酶和二肽基肽酶Ⅳ基因的筛选与多样性分析
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摘要
在日粮蛋白质的降解过程中，蛋白酶是蛋白质水解为肽或氨基酸的关键酶，由于受到纯培养技术的影响，瘤胃内分泌蛋白酶的细菌和各种蛋白酶的基因信息知之甚少。本试验旨在利用蛋白酶选择性培养基从瘤胃微生物Fosmid文库中筛选出含蛋白酶活性的克隆子，通过生物信息学分析获得这些克隆子的基因信息。应用脱脂乳粉和大豆蛋白粉两种蛋白酶选择性培养基，从30000个克隆中筛选得到14个具有蛋白酶活性的阳性克隆。利用福林酚试剂法检测14个蛋白酶克隆子的酶活力，结果表明每个克隆子分别具有不同的蛋白质分解能力。以酪蛋白为底物的克隆子酶活力介于0.59-2.74U/mg之间；以大豆蛋白粉为底物的克隆子酶活力在0.70-7.19U/mg之间。pro10F末端序列与金属肽酶匹配度为54%，属于肽酶M13家族，且该克隆蛋白酶最适pH值为7.0。选取两个克隆利用鸟枪测序法进行测序，经GenMark分析，共获得了53个不同的蛋白序列，其中有两个属于不同的肽酶家族的序列片段。
为了研究奶牛瘤胃内参与蛋白质降解过程中二肽基肽酶Ⅳ（dipeptidyl peptidases Ⅳ，DPP-Ⅳ）的序列特征和酶学性质，从奶牛瘤胃微生物Fosmid文库中利用简并引物筛选含DPP-Ⅳ的阳性克隆。提取阳性克隆粗酶液，利用Gly-Pro-pNA底物检测肽酶活性。筛选后获得10个含有DPP-Ⅳ的阳性克隆（命名为DP1-DP10）。Fosmid末端序列经BLASTX比对后，结果表明78%的序列可以与数据库的已知序列相匹配，但相似度变化较大（44%-94%）。DPP-Ⅳ序列经BioEdit比对后，结果表明均含有N端保守区域（D-W-V-Y-E-E-E）和C端催化区域（G-W-S-Y-G-G）。酶活力检测发现DP7肽酶活力最高，为6.88U·mg-1。提取质粒等量混合后用Illumina HiSeq2000进行建库测序，经过Glimmer软件分析，获得3591个基因，对这些基因进行功能注释，发现参与多种代谢途径的基因，尤其是参与蛋白质降解过程的基因，其中存在两个不同的DPP-Ⅳ基因，为瘤胃蛋白质代谢的进一步研究提供了基础信息。
选取10个阳性克隆中粗酶液活性最高的克隆DP7进行DPP-Ⅳ基因的研究。利用已有DP7中DPP-Ⅳ基因的序列两端设计引物，对DP7质粒进行直接测序，并对DPP-Ⅳ基因进行原核表达。结果发现DP7克隆中DPP-Ⅳ基因全长为2298bp，可编码756个氨基酸残基。利用预测的DPP-Ⅳ基因序列与GenBank数据库中的序列进行BLASTP比较，发现相似性最高的序列来源于Pontibacter sp的序列（46%），依次是Sphingobacterium sp（46%）、Solitalea canadensis（46%）、Marinilabilia sp（45%）和Cecembia lonarensi（s45%）。该序列具有DPP-Ⅳ三联体的催化结构（Ser633、Asp708和His740），且比其他的序列多了一段从422位到425位插入的氨基酸序列，说明该序列是一种新的DPP-Ⅳ基因序列。对该序列设计表达引物进行序列扩增，获得DPP-Ⅳ基因表达序列，经原核表达和纯化后，获得了DP7克隆中DPP-Ⅳ的目的蛋白，可继续进行DPP-Ⅳ酶学性质的研究。
为了解豆粕降解菌中DPP-Ⅳ基因的序列结构多样性，本试验利用尼龙袋法分别收集0、12、24和48h豆粕降解菌，提取总DNA，PCR扩增16S rDNA V3区进行变性梯度凝胶电泳分析，结果表明与0h相比，12、24和48h的豆粕降解菌存在明显的变化，0h细菌的菌群条带比其他时间点的菌群条带丰富。选取12h的豆粕降解菌作为DPP-Ⅳ基因简并引物的扩增模板，PCR产物克隆测序后，获得5个克隆的DPP-Ⅳ基因序列；经BioEdit软件对序列进行比对，分析发现这5条序列存在DPP-Ⅳ的保守区序列（D-W-V-Y-E-E-E），但催化区（G-X-S-X-X-G）存在S→T或S→R的变异。对不同时间点的豆粕降解菌DNA混合样品进行DPP-Ⅳ全长基因的扩增，获得20个克隆的DPP-Ⅳ基因的全长序列。20个克隆中DPP-Ⅳ基因序列长度均为2193bp，都具有DPP-Ⅳ的活性位点序列（G-X-S-X-X-G）和催化三联体结构，但在保守序列（D-W-V-N-E-E-E）区出现2个变异位点（V→A和N→S）。这4个变化位点的存在是否影响DPP-Ⅳ的酶活性有待进一步研究。
为了揭示体外培养条件下厌氧培养菌中DPP-Ⅳ基因多样性及莫能菌素对产生DPP-Ⅳ基因细菌的影响，本试验以酪蛋白为唯一氮源（P组），另一组在以酪蛋白为唯一氮源的基础上添加莫能菌素（M组），分别接种瘤胃液后，进行厌氧培养。培养12h后，收集培养液中的微生物，提取基因组DNA。利用设计的DPP-Ⅳ基因引物，通过PCR构建DPP-Ⅳ基因文库，挑取克隆测序后，获得66条DPP-Ⅳ基因序列；经Mothur软件分析发现23个OTU，其中OTU9可能是对莫能菌素敏感的蛋白降解菌的DPP-Ⅳ基因。对P和M组的厌氧培养菌进行DPP-Ⅳ基因的定量研究，发现P组的DPP-Ⅳ基因的拷贝数极显著高于M组（P<0.01）。这些结果表明莫能菌素影响了产DPP-Ⅳ细菌的数量。
During the degradative processing of diet protein, proteases are the key enzymes which hydrolyzeprotein to peptide or amino acid. However, little genetic information of protease originating from rumenmicrobiota is known due to the limitation of pure-cultured methods. To screen protease clones fromrumen microbial Fosmid library,14positive clones with protease activity were got by screening30000clones from skimmed milk powder's and soy protein powder's selective medium of proteases. Thezymolytic ability of protease from fourteen clones was measured by Folin-Phenol reagent method. Theresults showed that each clone had its unique ability of protease decomposition. The enzyme activityranged from0.59to2.74U/mg and from0.70to7.19U/mg with casein and isolated soybean protein asthe substrate respectively. The end sequences of pro10F have54%similarity with metal peptidasebelonged to peptidase family M13, and the optimal pH of the protease was7.0. Inserted fragments fromtwo clones were sequenced using shotgun sequencing method, and53different protein sequences weregained by GenMark analysis, two of which belonged to different peptidases family.
To characterize dipeptidyl peptidase Ⅳ (DPP-Ⅳ), the DPP-Ⅳ degenerate primers were used toscreen rumen microbial Fosmid library. The peptidase activity of extract crude enzyme from thepositive clones was measured using Gly-Pro-pNA as a substrate. Ten positive clones named DP1-DP10containing DPP-Ⅳ fragment were obtained.78%of the Fosmid end sequences could match with theknown genes (similarity44%-94%). DPP-Ⅳ sequences contained N-conservative region(D-W-V-Y-E-E-E) and C-catalytic domain (G-W-S-Y-G-G). The activity of DP7peptidase was highest(6.88U/mg). Plasmid of ten clones were extracted, mixed equal amounts and built screening pool, thensequenced by Illumina HiSeq2000.3591genes were obtained by Glimmer analysis. These genefunctions were annotated, and the results showed that these genes take part in various metabolicpathways. Particularly, two different DPP-Ⅳ genes participated in protein degradation. These resultsprovided basic information for further study of protein metabolic in the rumen.
The DPP-Ⅳ gene of DP7clone which had the highest peptidase activity of crude enzyme from tenclones was studied. Two primers were designed using DPP-Ⅳ gene (GenBank: JX466878) from DP7clone, plasmid of DP7clone was direct sequenced. The structural feature of DPP-Ⅳ gene was analyzedby bioinformatics method and DPP-Ⅳ gene was expressed in BL21competent cell. The analysis ofDPP-Ⅳ gene sequence showed it had one ORF with2298bp length (756amino acid residue)containing the characteristic catalytic domain G-W-S-F-G-G found in all known DPP-Ⅳs and theconserved region D-W-V-Y-E-E-E. The BLASTP analysis was done using the prediction of the DPP-Ⅳgene sequence comapring with GenBank database, and the results showed the highest similarity ofsequences derived from the sequence of Pontibacter sp DPP-Ⅳ (46%identity) followed bySphingobacterium sp DPP-Ⅳ (46%), Solitalea canadensis DPP-Ⅳ (46%), Marinilabilia sp (45%)andCecembia lonarensis (45%). DPP-Ⅳ had the identification of the catalytic triad (Ser-633, Asp-708andHis-740), and inserted with a length of amino acid sequence from422to445than that of other organisms. The results demonstrated DPP-Ⅳ gene obtained from DP7was a new sequence of DPP-Ⅳ.The DPP-Ⅳ gene expression sequence was obtain by PCR amplification from DP7clones usingsequence expression primer, and the target protein of DPP-Ⅳ was acquired by prokaryotic expressionand purification. The molecular weight of target protein was consistent with the predicted molecularweight (78kDa) indicating that could proceed with the study of DPP-Ⅳ enzymatic properties.
To understand the diversity of DPP-Ⅳ gene sequence structure derived from soybean mealdegradation bacteria, soybean meal degradation bacterium was collected at different time points (0,12,24and48h) by nylon bags technique. The total DNA was extracted, and then16S rDNA V3region wasamplified and analyzed using denaturing gel gradient electrophoresis (DGGE). Result showed thatsoybean meal degradation bacteria had obvious change at12,24and48h time points comparing to0h.Bands of bacteria flora at0h was richer than other time points, while bands at12h was larger than that24and48h. DNA of soybean meal degradation bacteria at12h was select as amplify templates ofDPP-Ⅳ gene degenerate primers. Five sequences of DPP-Ⅳ gene were obtained by PCR amplification,cloning and sequencing. ClustalW alignment showed that all five sequences had a conserved region(D-W-V-Y-E-E-E), but the characteristic catalytic domain (G-W-S-F-G-G) contained two mutations(S→T or R). By gene amplification, the full-length sequences of DPP-Ⅳ gene were acquired fromDNA mixed samples of soybean meal degradative bacteria at different time points. The length ofDPP-Ⅳ genes in twenty clones were2193bp. It contained the characteristic catalytic domain(G-W-S-F-G-G) and the catalytic triad composition, but the conserved region (D-W-V-Y-E-E-E) hadtwo mutations (V→A and N→S). The four mutations needed to be further study on whether affect theactivity of DPP-Ⅳ.
To reveal the genetic diversity of anaerobic bacterial DPP-Ⅳ gene in vitro cultivation and theinfluence of monensin in bacteria including DPP-Ⅳ gene, there were two group: one group substratewas casein (P), other group added monensin on the basis of casein (M). Anaerobic culture was doneafter inoculated with rumen fluid respectively. And then anaerobic bacterium was collected after12hculture and its DNA was extracted. DPP-Ⅳ gene library was established through PCR, and sixty-sixsequence of DPP-Ⅳ gene were obtained by sequencing the picking clones. Twenty-three operationaltaxonomic unit (OTU) were found by Mothur software analysis, and OTU9might be a DPP-Ⅳ gene ofprotein degradation bacteria sensitising to monensin. The copy number of DPP-Ⅳ gene in P group wassignificantly higher than that of M group (P<0.01) by quantitative analysis. These results suggested thatmonensin affected the number of bacteria included DPP-Ⅳ gene.
为了研究奶牛瘤胃内参与蛋白质降解过程中二肽基肽酶Ⅳ（dipeptidyl peptidases Ⅳ，DPP-Ⅳ）的序列特征和酶学性质，从奶牛瘤胃微生物Fosmid文库中利用简并引物筛选含DPP-Ⅳ的阳性克隆。提取阳性克隆粗酶液，利用Gly-Pro-pNA底物检测肽酶活性。筛选后获得10个含有DPP-Ⅳ的阳性克隆（命名为DP1-DP10）。Fosmid末端序列经BLASTX比对后，结果表明78%的序列可以与数据库的已知序列相匹配，但相似度变化较大（44%-94%）。DPP-Ⅳ序列经BioEdit比对后，结果表明均含有N端保守区域（D-W-V-Y-E-E-E）和C端催化区域（G-W-S-Y-G-G）。酶活力检测发现DP7肽酶活力最高，为6.88U·mg-1。提取质粒等量混合后用Illumina HiSeq2000进行建库测序，经过Glimmer软件分析，获得3591个基因，对这些基因进行功能注释，发现参与多种代谢途径的基因，尤其是参与蛋白质降解过程的基因，其中存在两个不同的DPP-Ⅳ基因，为瘤胃蛋白质代谢的进一步研究提供了基础信息。
选取10个阳性克隆中粗酶液活性最高的克隆DP7进行DPP-Ⅳ基因的研究。利用已有DP7中DPP-Ⅳ基因的序列两端设计引物，对DP7质粒进行直接测序，并对DPP-Ⅳ基因进行原核表达。结果发现DP7克隆中DPP-Ⅳ基因全长为2298bp，可编码756个氨基酸残基。利用预测的DPP-Ⅳ基因序列与GenBank数据库中的序列进行BLASTP比较，发现相似性最高的序列来源于Pontibacter sp的序列（46%），依次是Sphingobacterium sp（46%）、Solitalea canadensis（46%）、Marinilabilia sp（45%）和Cecembia lonarensi（s45%）。该序列具有DPP-Ⅳ三联体的催化结构（Ser633、Asp708和His740），且比其他的序列多了一段从422位到425位插入的氨基酸序列，说明该序列是一种新的DPP-Ⅳ基因序列。对该序列设计表达引物进行序列扩增，获得DPP-Ⅳ基因表达序列，经原核表达和纯化后，获得了DP7克隆中DPP-Ⅳ的目的蛋白，可继续进行DPP-Ⅳ酶学性质的研究。
为了解豆粕降解菌中DPP-Ⅳ基因的序列结构多样性，本试验利用尼龙袋法分别收集0、12、24和48h豆粕降解菌，提取总DNA，PCR扩增16S rDNA V3区进行变性梯度凝胶电泳分析，结果表明与0h相比，12、24和48h的豆粕降解菌存在明显的变化，0h细菌的菌群条带比其他时间点的菌群条带丰富。选取12h的豆粕降解菌作为DPP-Ⅳ基因简并引物的扩增模板，PCR产物克隆测序后，获得5个克隆的DPP-Ⅳ基因序列；经BioEdit软件对序列进行比对，分析发现这5条序列存在DPP-Ⅳ的保守区序列（D-W-V-Y-E-E-E），但催化区（G-X-S-X-X-G）存在S→T或S→R的变异。对不同时间点的豆粕降解菌DNA混合样品进行DPP-Ⅳ全长基因的扩增，获得20个克隆的DPP-Ⅳ基因的全长序列。20个克隆中DPP-Ⅳ基因序列长度均为2193bp，都具有DPP-Ⅳ的活性位点序列（G-X-S-X-X-G）和催化三联体结构，但在保守序列（D-W-V-N-E-E-E）区出现2个变异位点（V→A和N→S）。这4个变化位点的存在是否影响DPP-Ⅳ的酶活性有待进一步研究。
为了揭示体外培养条件下厌氧培养菌中DPP-Ⅳ基因多样性及莫能菌素对产生DPP-Ⅳ基因细菌的影响，本试验以酪蛋白为唯一氮源（P组），另一组在以酪蛋白为唯一氮源的基础上添加莫能菌素（M组），分别接种瘤胃液后，进行厌氧培养。培养12h后，收集培养液中的微生物，提取基因组DNA。利用设计的DPP-Ⅳ基因引物，通过PCR构建DPP-Ⅳ基因文库，挑取克隆测序后，获得66条DPP-Ⅳ基因序列；经Mothur软件分析发现23个OTU，其中OTU9可能是对莫能菌素敏感的蛋白降解菌的DPP-Ⅳ基因。对P和M组的厌氧培养菌进行DPP-Ⅳ基因的定量研究，发现P组的DPP-Ⅳ基因的拷贝数极显著高于M组（P<0.01）。这些结果表明莫能菌素影响了产DPP-Ⅳ细菌的数量。
During the degradative processing of diet protein, proteases are the key enzymes which hydrolyzeprotein to peptide or amino acid. However, little genetic information of protease originating from rumenmicrobiota is known due to the limitation of pure-cultured methods. To screen protease clones fromrumen microbial Fosmid library,14positive clones with protease activity were got by screening30000clones from skimmed milk powder's and soy protein powder's selective medium of proteases. Thezymolytic ability of protease from fourteen clones was measured by Folin-Phenol reagent method. Theresults showed that each clone had its unique ability of protease decomposition. The enzyme activityranged from0.59to2.74U/mg and from0.70to7.19U/mg with casein and isolated soybean protein asthe substrate respectively. The end sequences of pro10F have54%similarity with metal peptidasebelonged to peptidase family M13, and the optimal pH of the protease was7.0. Inserted fragments fromtwo clones were sequenced using shotgun sequencing method, and53different protein sequences weregained by GenMark analysis, two of which belonged to different peptidases family.
To characterize dipeptidyl peptidase Ⅳ (DPP-Ⅳ), the DPP-Ⅳ degenerate primers were used toscreen rumen microbial Fosmid library. The peptidase activity of extract crude enzyme from thepositive clones was measured using Gly-Pro-pNA as a substrate. Ten positive clones named DP1-DP10containing DPP-Ⅳ fragment were obtained.78%of the Fosmid end sequences could match with theknown genes (similarity44%-94%). DPP-Ⅳ sequences contained N-conservative region(D-W-V-Y-E-E-E) and C-catalytic domain (G-W-S-Y-G-G). The activity of DP7peptidase was highest(6.88U/mg). Plasmid of ten clones were extracted, mixed equal amounts and built screening pool, thensequenced by Illumina HiSeq2000.3591genes were obtained by Glimmer analysis. These genefunctions were annotated, and the results showed that these genes take part in various metabolicpathways. Particularly, two different DPP-Ⅳ genes participated in protein degradation. These resultsprovided basic information for further study of protein metabolic in the rumen.
The DPP-Ⅳ gene of DP7clone which had the highest peptidase activity of crude enzyme from tenclones was studied. Two primers were designed using DPP-Ⅳ gene (GenBank: JX466878) from DP7clone, plasmid of DP7clone was direct sequenced. The structural feature of DPP-Ⅳ gene was analyzedby bioinformatics method and DPP-Ⅳ gene was expressed in BL21competent cell. The analysis ofDPP-Ⅳ gene sequence showed it had one ORF with2298bp length (756amino acid residue)containing the characteristic catalytic domain G-W-S-F-G-G found in all known DPP-Ⅳs and theconserved region D-W-V-Y-E-E-E. The BLASTP analysis was done using the prediction of the DPP-Ⅳgene sequence comapring with GenBank database, and the results showed the highest similarity ofsequences derived from the sequence of Pontibacter sp DPP-Ⅳ (46%identity) followed bySphingobacterium sp DPP-Ⅳ (46%), Solitalea canadensis DPP-Ⅳ (46%), Marinilabilia sp (45%)andCecembia lonarensis (45%). DPP-Ⅳ had the identification of the catalytic triad (Ser-633, Asp-708andHis-740), and inserted with a length of amino acid sequence from422to445than that of other organisms. The results demonstrated DPP-Ⅳ gene obtained from DP7was a new sequence of DPP-Ⅳ.The DPP-Ⅳ gene expression sequence was obtain by PCR amplification from DP7clones usingsequence expression primer, and the target protein of DPP-Ⅳ was acquired by prokaryotic expressionand purification. The molecular weight of target protein was consistent with the predicted molecularweight (78kDa) indicating that could proceed with the study of DPP-Ⅳ enzymatic properties.
To understand the diversity of DPP-Ⅳ gene sequence structure derived from soybean mealdegradation bacteria, soybean meal degradation bacterium was collected at different time points (0,12,24and48h) by nylon bags technique. The total DNA was extracted, and then16S rDNA V3region wasamplified and analyzed using denaturing gel gradient electrophoresis (DGGE). Result showed thatsoybean meal degradation bacteria had obvious change at12,24and48h time points comparing to0h.Bands of bacteria flora at0h was richer than other time points, while bands at12h was larger than that24and48h. DNA of soybean meal degradation bacteria at12h was select as amplify templates ofDPP-Ⅳ gene degenerate primers. Five sequences of DPP-Ⅳ gene were obtained by PCR amplification,cloning and sequencing. ClustalW alignment showed that all five sequences had a conserved region(D-W-V-Y-E-E-E), but the characteristic catalytic domain (G-W-S-F-G-G) contained two mutations(S→T or R). By gene amplification, the full-length sequences of DPP-Ⅳ gene were acquired fromDNA mixed samples of soybean meal degradative bacteria at different time points. The length ofDPP-Ⅳ genes in twenty clones were2193bp. It contained the characteristic catalytic domain(G-W-S-F-G-G) and the catalytic triad composition, but the conserved region (D-W-V-Y-E-E-E) hadtwo mutations (V→A and N→S). The four mutations needed to be further study on whether affect theactivity of DPP-Ⅳ.
To reveal the genetic diversity of anaerobic bacterial DPP-Ⅳ gene in vitro cultivation and theinfluence of monensin in bacteria including DPP-Ⅳ gene, there were two group: one group substratewas casein (P), other group added monensin on the basis of casein (M). Anaerobic culture was doneafter inoculated with rumen fluid respectively. And then anaerobic bacterium was collected after12hculture and its DNA was extracted. DPP-Ⅳ gene library was established through PCR, and sixty-sixsequence of DPP-Ⅳ gene were obtained by sequencing the picking clones. Twenty-three operationaltaxonomic unit (OTU) were found by Mothur software analysis, and OTU9might be a DPP-Ⅳ gene ofprotein degradation bacteria sensitising to monensin. The copy number of DPP-Ⅳ gene in P group wassignificantly higher than that of M group (P<0.01) by quantitative analysis. These results suggested thatmonensin affected the number of bacteria included DPP-Ⅳ gene.
引文
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